If the MSG source is a PST file, then the MSG file exported will, in essence, be a new file created from the PST rather than an existing MSG file (if it was a loose file).
The MD5 number will change when a message file from a PST source is exported. When Clearwell performs a metadata export with natives checked for the export, Clearwell is is essentially extracting the MSG from the PST at that point in time. The system has an internal logic which is used to calculate MD5 hash based on certain attributes.
If the same MSG is exported some time later, the system will recalculate the MD5 hash, which is per design. Since MD5 hashes are calculated by Clearwell, they do not necessarily have to be the same for the exact same message coming from a PST.
This is normal behavior as the MSG file is changed when it is extracted from the PST file for the export.
Each time it is extracted from the PST source, the metadata value of the MSG's"PR_LAST_MODIFICATION_TIME" and "PR_CREATION_TIME" are altered, which will change the MD5 value.
If the MSG file is a loose file, then the MD5 is not adjusted and will remain the same.